Ryan Poplin 98f18b5f9e Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.		2012-12-17 11:27:44 -05:00
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downsampling	Fixes for bugs uncovered by unit tests	2012-11-06 16:07:40 -08:00
walkers	Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.	2012-12-17 11:27:44 -05:00